Designing and Building a Framework for DNA Sequence Alignment Using Grid Computing
Journal Title: International Journal of Advanced Computer Science & Applications - Year 2014, Vol 5, Issue 9
Abstract
Deoxyribonucleic acid (DNA) is a molecule that encodes unique genetic instructions used in the development and functioning of all known living organisms and many viruses. This Genetic information is encoded as a sequence of nucleotides (adenine, cytosine, guanine, and thymine) recorded using the letters A, C, G, and T.DNA querying or alignment of these sequences required dynamic programming tools and very complex matrices and some heuristic methods like FASTA and BLAST that use massive force of processing and highly time consuming. We present a parallel solution to reduce the processing time. Smith waterman algorithm, Needleman-Wunsch, some weighting matrices and a grid of computers are used to find field of similarity between these sequences in large DNA datasets. This grid consists of master computer and unlimited number of agents. The master computer is the user interface for insert the queried sequence and coordinates the processing between the grid agents.
Authors and Affiliations
EL-Sayed Orabi, Mohamed Assal, Mustafa Azim, Yasser Kamal
Keywords
Related Articles
- EP ID EP163055
- DOI 10.14569/IJACSA.2014.050913
- Views 114
- Downloads 0
Object Conveyance Algorithm for Multiple Mobile Robots based on Object Shape and Size
This paper describes a determination method of a number of a team for multiple mobile robot object conveyance. The number of robot on multiple mobile robot systems is the factor of complexity on robots formation and moti...
Threshold Based Penalty Functions for Constrained Multiobjective Optimization
This paper compares the performance of our re-cently proposed threshold based penalty function against its dynamic and adaptive variants. These penalty functions are incorporated in the update and replacement scheme of t...
Video Transmission over Cognitive Radio TDMA Networks under Collision Errors
Cognitive Radio (CR) networks are emerging as new paradigm of communication and channels sharing in multimedia and wireless networks. In this paper, we address the problem of video transmission over shared CR netwo...
Computer Vision for Screening Resistance Level of Rice Varieties to Brown Planthopper
Brown planthopper is one of the most important insect pest that threatens the stability of national rice production in Indonesia. One of the efforts to save rice production is by using brown planthopper resistant variety...
The Performance between XEN-HVM, XEN-PV and Open-VZ during live-migration
The aim of this paper is to compare the performance between three hypervisors: XEN-PV, XEN-HVM and Open-VZ. We have simulated the migration of a virtual machine by using a warning failure approach. Based on some experime...